|
Status |
Public on Jun 01, 2009 |
Title |
Normal stroma, slide 9538, sample 1 |
Sample type |
RNA |
|
|
Channel 1 |
Source name |
normal prostate stroma
|
Organism |
Homo sapiens |
Characteristics |
normal peripheral zone prostate stroma
|
Extracted molecule |
total RNA |
Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions. Microarray analysis was performed using 2.5 micrograms of total RNA.
|
Label |
Alexa Fluor 647
|
Label protocol |
Complementary DNA (cDNA) reverse transcription and fluorescent labeling reactions were carried out using SuperScript Plus Direct cDNA Labeling system (Invitrogen, Carlsbad, CA).
|
|
|
Channel 2 |
Source name |
human, universal reference RNA
|
Organism |
Homo sapiens |
Characteristics |
Stratagene, Universal Human Reference RNA Catalog #740000
|
Extracted molecule |
total RNA |
Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions. Microarray analysis was performed using 2.5 micrograms of total RNA.
|
Label |
Alexa Fluor 555
|
Label protocol |
Complementary DNA (cDNA) reverse transcription and fluorescent labeling reactions were carried out using SuperScript Plus Direct cDNA Labeling system (Invitrogen, Carlsbad, CA).
|
|
|
|
Hybridization protocol |
The sample and reference probes were mixed with GEx hybridization buffer and blocking solution (Agilent, Santa Clara, CA) and denatured by a 2-minute incubation at 95 degC. Probes were hybridized to Agilent 4x44K Whole Human Genome arrays and rotating over night at 65 degC.
|
Scan protocol |
Slide were scanned in an Agilent Microarray Scanner and the data were analyzed using Agilent Feature Extraction Software (v.9.1).
|
Description |
human normal peripheral zone prostate stroma, compared to universal reference RNA
|
Data processing |
LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent and Bioconductor software was used.
|
|
|
Submission date |
Jun 04, 2008 |
Last update date |
Jan 16, 2009 |
Contact name |
Chad Creighton |
E-mail(s) |
creighto@bcm.tmc.edu
|
Organization name |
Baylor College of Medicine
|
Department |
Biostatistics, Ducan Cancer Center
|
Street address |
One Baylor Plaza, Mail Stop: BCM305
|
City |
Houston |
State/province |
TX |
ZIP/Postal code |
77030 |
Country |
USA |
|
|
Platform ID |
GPL4133 |
Series (1) |
GSE11682 |
Gene expression profiles of reactive stroma in prostate cancer |
|